some naming changs

shenwei356 · Nov 20, 2014 · 6d041f4 · 6d041f4
1 parent 613ff8c
commit 6d041f4
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Showing 19 changed files with 13 additions and 11 deletions.
diff --git a/blast/rename_fasta_head_before_blast.pl → blast/fasta_rename_head_before_blast.pl b/blast/rename_fasta_head_before_blast.pl → blast/fasta_rename_head_before_blast.pl
@@ -5,15 +5,7 @@
 # Date    : 2014-08-14
 
 use strict;
-
-# try to use BioUtil::Seq
-if ( eval { require BioUtil::Seq; 1; } ne 1 ) {
-    die "\nPlease install BioUtil::Seq by CPAN:\n"
-        . "  cpan install BioUtil::Seq\n\n";
-}
-else {
-    BioUtil::Seq->import();
-}
+use BioUtil::Seq;
 
 die "\nUsage: $0 fasta_file [fasta_file ...]\n\n"
     unless @ARGV > 0;

diff --git a/enzyme/.directory b/enzyme/.directory
@@ -0,0 +1,4 @@
+[Dolphin]
+Timestamp=2014,11,20,13,13,9
+Version=3
+ViewMode=1
diff --git a/enzyme/check_digested_sequence_number.pl → ...estrict_check_digested_sequence_number.pl b/enzyme/check_digested_sequence_number.pl → ...estrict_check_digested_sequence_number.pl
diff --git a/enzyme/find_enzymes_with_T_tail.pl → enzyme/restrict_with_T_tail.pl b/enzyme/find_enzymes_with_T_tail.pl → enzyme/restrict_with_T_tail.pl
diff --git a/...find_enzymes_with_far_away_digest_site.pl → enzyme/restrict_with_far_away_digest_site.pl b/...find_enzymes_with_far_away_digest_site.pl → enzyme/restrict_with_far_away_digest_site.pl
diff --git a/...zymes_without_digest_site_in_sequences.pl → ...trict_without_digest_site_in_sequences.pl b/...zymes_without_digest_site_in_sequences.pl → ...trict_without_digest_site_in_sequences.pl
diff --git a/util/.directory → for_education/.directory b/util/.directory → for_education/.directory
diff --git a/util/Parsing grouped data in multi-line.pl → ...ion/Parsing grouped data in multi-line.pl b/util/Parsing grouped data in multi-line.pl → ...ion/Parsing grouped data in multi-line.pl
diff --git a/...equence_by_id_file(for education_only).pl → ...tion/fasta_extract_sequence_by_id_file.pl b/...equence_by_id_file(for education_only).pl → ...tion/fasta_extract_sequence_by_id_file.pl
diff --git a/util/simple_statistics.pl → for_education/simple_statistics.pl b/util/simple_statistics.pl → for_education/simple_statistics.pl
diff --git a/protein/.directory b/protein/.directory
@@ -0,0 +1,4 @@
+[Dolphin]
+Timestamp=2014,11,20,13,13,30
+Version=3
+ViewMode=1
diff --git a/protein/batch_compute_pI.pl → protein/protein_batch_compute_pI.pl b/protein/batch_compute_pI.pl → protein/protein_batch_compute_pI.pl
diff --git a/sequence/common_seqs.pl → sequence/fasta_common_seqs.pl b/sequence/common_seqs.pl → sequence/fasta_common_seqs.pl
diff --git a/sequence/common_seqs2.pl → sequence/fasta_common_seqs2.pl b/sequence/common_seqs2.pl → sequence/fasta_common_seqs2.pl
diff --git a/sequence/extract_sequence_by_pattern.pl → sequence/fasta_extract_by_pattern.pl b/sequence/extract_sequence_by_pattern.pl → sequence/fasta_extract_by_pattern.pl
diff --git a/sequence/extract_sequence_randomly.pl → sequence/fasta_extract_randomly.pl b/sequence/extract_sequence_randomly.pl → sequence/fasta_extract_randomly.pl
diff --git a/sequence/format_fasta.pl → sequence/fasta_format.pl b/sequence/format_fasta.pl → sequence/fasta_format.pl
diff --git a/sequence/fasta_seq_length.py b/sequence/fasta_seq_length.py
@@ -1,4 +1,6 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
+from __future__ import print_function
+
 import sys
 import os
 
@@ -30,4 +32,4 @@
 
 mpl.rc("figure", figsize=(8, 4))
 sns.distplot(lengths)
-plt.savefig(file + ".len.png")
+plt.savefig(file + ".len.png")
diff --git a/sequence/extract_paired_reads.pl → sequence/fastq_extract_paired_reads.pl b/sequence/extract_paired_reads.pl → sequence/fastq_extract_paired_reads.pl