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root/scriptome/all_params.tab
Revision: 1.4
Committed: Tue Jul 7 18:52:50 2009 UTC (7 years, 5 months ago) by amirkarger
Branch: MAIN
CVS Tags: HEAD
Changes since 1.3: +3 -0 lines
Log Message:
* Tweak Makefile
* Add change_split_fasta tool (Change.pod, all_params)
* html2scriptome wasn't handling q{} correctly (tidy() broke it)
* Make t/*.pl use dated sample file dir
* Remove unneeded BEGIN from choose_lines_col_more_than_limit

Line File contents
1 calc_col_sum $col Variable Column to sum $col=1
2 calc_col_sum file.tab Input file(s) file.tab
3 calc_col_length $col Variable Column to measure length of $col = 2
4 calc_col_length seqs.tab Input file(s) seqs.tab > seqs_length.tab
5 calc_col_length seqs_length.tab Output file seqs.tab > seqs_length.tab
6 calc_line_numbers $separator Variable What to print between line number and rest of line - \t means tab $separator= qq~\t~;
7 calc_line_numbers gene_list.txt Input file(s) gene_list.txt > numbered_gene_list.txt
8 calc_line_numbers numbered_gene_list.txt Output file gene_list.txt > numbered_gene_list.txt
9 calc_row_sum @cols Variable Which column(s) to add "@cols=(1, 2, 3)"
10 calc_row_sum in.tab Input file(s) in.tab > out.tab
11 calc_row_sum out.tab Output file in.tab > out.tab
12 calc_repeats_for_each_value_in_col $col Variable Column to count repeats in $col = 1
13 calc_repeats_for_each_value_in_col gene_go.txt Input file(s) gene_go.txt > go_repeats.txt
14 calc_repeats_for_each_value_in_col go_repeats.txt Output file gene_go.txt > go_repeats.txt
15 calc_sum_of_col_for_groups_of_lines $value_col Variable Column to determine grouping of lines $value_col=0; $sum_col=2;
16 calc_sum_of_col_for_groups_of_lines $sum_col Variable Column to sum for sets of similar lines $value_col=0; $sum_col=2;
17 calc_sum_of_col_for_groups_of_lines exon_length.tab Input file(s) exon_length.tab > gene_length.tab
18 calc_sum_of_col_for_groups_of_lines gene_length.tab Output file exon_length.tab > gene_length.tab
19 calc_num_lines gene_list.txt Input file(s) gene_list.txt > gene_count.txt
20 calc_num_lines gene_count.txt Output file gene_list.txt > gene_count.txt
21 calc_num_fasta_records seqs.fasta Input file(s) seqs.fasta > seqs_count.txt
22 calc_num_fasta_records seqs_count.txt Output file seqs.fasta > seqs_count.txt
23 change_any_separator_to_tab $sep Variable Character(s) to change to tab "$sep= qq~,~"
24 change_any_separator_to_tab file.csv Input file(s) file.csv > file.tab
25 change_any_separator_to_tab file.tab Output file file.csv > file.tab
26 change_tab_to_any_separator $sep Variable Character(s) to change tab to "$sep= qq~,~"
27 change_tab_to_any_separator file.tab Input file(s) file.tab > file.csv
28 change_tab_to_any_separator file.csv Output file file.tab > file.csv
29 change_remove_spaces file.spaces Input file(s) file.spaces > file.nospace
30 change_remove_spaces file.nospace Output file file.spaces > file.nospace
31 change_upper_case file.mixed Input file(s) file.mixed > file.uc
32 change_upper_case file.uc Output file file.mixed > file.uc
33 change_fasta_to_tab seqs.fna Input file(s) seqs.fna > seqs.tab
34 change_fasta_to_tab seqs.tab Output file seqs.fna > seqs.tab
35 change_tab_to_fasta seqs.tab Input file(s) seqs.tab > seqs.fasta
36 change_tab_to_fasta seqs.fasta Output file seqs.tab > seqs.fasta
37 change_bio_format_to_bio_format $informat Variable Input file format $informat = qq~genbank~; $outformat = qq~fasta~;
38 change_bio_format_to_bio_format $outformat Variable Output file format $informat = qq~genbank~; $outformat = qq~fasta~;
39 change_bio_format_to_bio_format myseqs.genbank Input file(s) myseqs.genbank > myseqs.fasta
40 change_bio_format_to_bio_format myseqs.fasta Output file myseqs.genbank > myseqs.fasta
41 change_transpose_table original.tab Input file(s) original.tab > transposed.tab
42 change_transpose_table transposed.tab Output file original.tab > transposed.tab
43 change_split_fasta $split_seqs Variable Number of sequences per output file $split_seqs = 3; $out_template = qq~small_NUMBER.fasta~;
44 change_split_fasta $out_template Variable Template for output file name $split_seqs = 3; $out_template = qq~small_NUMBER.fasta~;
45 change_split_fasta big.fasta Input file(s) big.fasta
46 choose_cols @cols Variable Column(s) to choose (in desired order) "@cols=(1, -1, 2)"
47 choose_cols all_cols Input file(s) all_cols > some_cols_chosen
48 choose_cols some_cols_chosen Output file all_cols > some_cols_chosen
49 choose_cols_to_delete @del_col Variable Column(s) to delete "@del_col = (0, 3..6, -1)"
50 choose_cols_to_delete all_cols Input file(s) all_cols > some_cols_deleted
51 choose_cols_to_delete some_cols_deleted Output file all_cols > some_cols_deleted
52 choose_lines_matching_text $string Variable Text to match $string=q{>CG};
53 choose_lines_matching_text a.fsa Input file(s) a.fsa > descs
54 choose_lines_matching_text descs Output file a.fsa > descs
55 choose_nonempty_lines a.fasta Input file(s) a.fasta > noblanks.fasta
56 choose_nonempty_lines noblanks.fasta Output file a.fasta > noblanks.fasta
57 choose_lines_col_more_than_limit $col Variable Column to limit $col=-1; $limit=80;
58 choose_lines_col_more_than_limit $limit Variable Minimum value in column $col=-1; $limit=80;
59 choose_lines_col_more_than_limit all.blast Input file(s) all.blast > only_big.blast
60 choose_lines_col_more_than_limit only_big.blast Output file all.blast > only_big.blast
61 choose_lines_col_less_than_limit $col Variable Column to limit $col=-2; $limit=1e-10;
62 choose_lines_col_less_than_limit $limit Variable Maximum value in column $col=-2; $limit=1e-10;
63 choose_lines_col_less_than_limit all.blast Input file(s) all.blast > only_small.blast
64 choose_lines_col_less_than_limit only_small.blast Output file all.blast > only_small.blast
65 choose_lines_with_col_max $col Variable Column to find maximum in $col=1
66 choose_lines_with_col_max fold_change.tab Input file(s) fold_change.tab > col_max.tab
67 choose_lines_with_col_max col_max.tab Output file fold_change.tab > col_max.tab
68 choose_lines_with_col_min $col Variable Column to find minimum in $col=1
69 choose_lines_with_col_min blast.tab Input file(s) blast.tab > col_min.tab
70 choose_lines_with_col_min col_min.tab Output file blast.tab > col_min.tab
71 choose_lines_with_max_per_name $name_col Variable Column with identifiers / names $name_col=0;
72 choose_lines_with_max_per_name $score_col Variable Column with scores / values $score_col=2;
73 choose_lines_with_max_per_name blast.tab Input file(s) blast.tab > best_hits.tab
74 choose_lines_with_max_per_name best_hits.tab Output file blast.tab > best_hits.tab
75 choose_lines_with_min_per_name $name_col Variable Column with identifiers / names $name_col=0;
76 choose_lines_with_min_per_name $score_col Variable Column with scores / values $score_col=-2;
77 choose_lines_with_min_per_name blast.tab Input file(s) blast.tab > best_hits.tab
78 choose_lines_with_min_per_name best_hits.tab Output file blast.tab > best_hits.tab
79 choose_lines_col_m_equals_col_n_alpha $colm Variable Text column to compare $colm=0; $coln=1;
80 choose_lines_col_m_equals_col_n_alpha $coln Variable Other text column to compare $colm=0; $coln=1;
81 choose_lines_col_m_equals_col_n_alpha infile Input file(s) infile > outfile
82 choose_lines_col_m_equals_col_n_alpha outfile Output file infile > outfile
83 choose_lines_col_m_equals_col_n_num $colm Variable Numerical column to compare $colm=0; $coln=1;
84 choose_lines_col_m_equals_col_n_num $coln Variable Other numerical column to compare $colm=0; $coln=1;
85 choose_lines_col_m_equals_col_n_num infile Input file(s) infile > outfile
86 choose_lines_col_m_equals_col_n_num outfile Output file infile > outfile
87 choose_lines_col_m_more_than_col_n $colm Variable Numerical column to compare $colm=0; $coln=1;
88 choose_lines_col_m_more_than_col_n $coln Variable Other numerical column to compare $colm=0; $coln=1;
89 choose_lines_col_m_more_than_col_n infile Input file(s) infile > outfile
90 choose_lines_col_m_more_than_col_n outfile Output file infile > outfile
91 choose_first_n_lines $num_lines Variable Number of lines to choose $num_lines=2;
92 choose_first_n_lines infile Input file(s) infile > outfile
93 choose_first_n_lines outfile Output file infile > outfile
94 choose_last_n_lines $num_lines Variable Number of lines to choose $num_lines=2;
95 choose_last_n_lines infile Input file(s) infile > outfile
96 choose_last_n_lines outfile Output file infile > outfile
97 choose_all_but_first_n_lines $del_lines Variable Number of lines to delete $del_lines=1;
98 choose_all_but_first_n_lines infile Input file(s) infile > outfile
99 choose_all_but_first_n_lines outfile Output file infile > outfile
100 choose_unique_lines genes Input file(s) genes > unique
101 choose_unique_lines unique Output file genes > unique
102 choose_unique_lines_by_col $column Variable Column in which to look for unique values $column = 0
103 choose_unique_lines_by_col hits Input file(s) hits > unique_hits
104 choose_unique_lines_by_col unique_hits Output file hits > unique_hits
105 choose_unique_FASTA a.fsa Input file(s) a.fsa > unique.fsa
106 choose_unique_FASTA unique.fsa Output file a.fsa > unique.fsa
107 choose_FASTAs_from_list id_list Input file(s) File with FASTA identifiers (no > signs) id_list a.fsa > found.fsa
108 choose_FASTAs_from_list a.fsa Input file(s) FASTA file id_list a.fsa > found.fsa
109 choose_FASTAs_from_list found.fsa Output file id_list a.fsa > found.fsa
110 fetch_sequence_web $database Variable Database name $database= qq~swiss~; $id= qq~ROA1_HUMAN~; $format= qq~fasta~;
111 fetch_sequence_web $id Variable Identifier $database= qq~swiss~; $id= qq~ROA1_HUMAN~; $format= qq~fasta~;
112 fetch_sequence_web $format Variable Format to write sequence in $database= qq~swiss~; $id= qq~ROA1_HUMAN~; $format= qq~fasta~;
113 fetch_sequence_web seq.fasta Output file > seq.fasta
114 fetch_file_web $web_file Variable Web address $web_file = qq~ftp://ftp.ncbi.nih.gov/genbank/GB_Release_Number~; $store = qq~GB.txt~;
115 fetch_file_web $store Variable Name of file to save to $web_file = qq~ftp://ftp.ncbi.nih.gov/genbank/GB_Release_Number~; $store = qq~GB.txt~;
116 merge_files_union file1.txt Input file(s) First file file1.txt file2.txt > union.txt
117 merge_files_union file2.txt Input file(s) Second file file1.txt file2.txt > union.txt
118 merge_files_union union.txt Output file file1.txt file2.txt > union.txt
119 merge_files_intersection file1.txt Input file(s) First file file1.txt file2.txt > intersection.txt
120 merge_files_intersection file2.txt Input file(s) Second file file1.txt file2.txt > intersection.txt
121 merge_files_intersection intersection.txt Output file file1.txt file2.txt > intersection.txt
122 merge_files_lines_not_in_both xor1 Input file(s) First file xor1 xor2 > not_shared
123 merge_files_lines_not_in_both xor2 Input file(s) Second file xor1 xor2 > not_shared
124 merge_files_lines_not_in_both not_shared Output file xor1 xor2 > not_shared
125 merge_files_lines_only_in_first yes_list Input file(s) Take lines in this file yes_list no_list > only_yes
126 merge_files_lines_only_in_first no_list Input file(s) Exclude lines in this file yes_list no_list > only_yes
127 merge_files_lines_only_in_first only_yes Output file yes_list no_list > only_yes
128 merge_lines_based_on_shared_column $col1 Variable Column in first file $col1=1; $col2=0;
129 merge_lines_based_on_shared_column $col2 Variable Column in second file $col1=1; $col2=0;
130 merge_lines_based_on_shared_column ortho.tab Input file(s) First file ortho.tab human_func.tab > fly_func.tab
131 merge_lines_based_on_shared_column human_func.tab Input file(s) Second file ortho.tab human_func.tab > fly_func.tab
132 merge_lines_based_on_shared_column fly_func.tab Output file ortho.tab human_func.tab > fly_func.tab
133 merge_lines_side_by_side $separator Variable Separator between lines from file1 and file2 $separator=qq"\t";
134 merge_lines_side_by_side annotations.tab Input file(s) First file annotations.tab
135 merge_lines_side_by_side ids.tab Input file(s) Second file ids.tab
136 merge_lines_side_by_side annotations_and_ids.tab Output file annotations_and_ids.tab
137 sort_alpha_asc unsorted Input file(s) unsorted > sorted_asc
138 sort_alpha_asc sorted_asc Output file unsorted > sorted_asc
139 sort_alpha_desc unsorted Input file(s) unsorted > sorted_desc
140 sort_alpha_desc sorted_desc Output file unsorted > sorted_desc
141 sort_nocase_asc unsorted Input file(s) unsorted > sorted_nc_asc
142 sort_nocase_asc sorted_nc_asc Output file unsorted > sorted_nc_asc
143 sort_nocase_desc unsorted Input file(s) unsorted > sorted_nc_desc
144 sort_nocase_desc sorted_nc_desc Output file unsorted > sorted_nc_desc
145 sort_num_asc unsorted Input file(s) unsorted > sorted_num_asc
146 sort_num_asc sorted_num_asc Output file unsorted > sorted_num_asc
147 sort_num_desc unsorted Input file(s) unsorted > sorted_num_desc
148 sort_num_desc sorted_num_desc Output file unsorted > sorted_num_desc
149 sort_on_column_num $column Variable Numerical column to sort by $column = 1;
150 sort_on_column_num unsorted Input file(s) unsorted > sorted_col
151 sort_on_column_num sorted_col Output file unsorted > sorted_col
152 sort_on_column_num_desc $column Variable Numerical column to sort by $column = 1;
153 sort_on_column_num_desc unsorted Input file(s) unsorted > sorted_col
154 sort_on_column_num_desc sorted_col Output file unsorted > sorted_col
155 sort_on_column_alpha $column Variable Text column to sort by $column = 1;
156 sort_on_column_alpha unsorted Input file(s) unsorted > sorted_col
157 sort_on_column_alpha sorted_col Output file unsorted > sorted_col
158 sort_on_column_alpha_desc $column Variable Text column to sort by $column = 1;
159 sort_on_column_alpha_desc unsorted Input file(s) unsorted > sorted_col
160 sort_on_column_alpha_desc sorted_col Output file unsorted > sorted_col
161 help_solve_all_my_problems $param1 Variable Important text $param1=qq~something~;
162 help_solve_all_my_problems $param2 Variable Important number $param2=37;
163 help_solve_all_my_problems infile1 Input file(s) One important file infile1 infile2 > outfile
164 help_solve_all_my_problems infile2 Input file(s) Other important file infile1 infile2 > outfile
165 help_solve_all_my_problems outfile Output file Results go here infile1 infile2 > outfile