Merge pull request #50 from SysBioChalmers/Dev

Dev

Author: hongzhonglu

…gn/A0_translate_aln_codon_to_aa_macse.sh …gn/A1_translate_aln_codon_to_aa_macse.shevolution_analysis/code/code_align/A0_translate_aln_codon_to_aa_macse.sh renamed to evolution_analysis/code/code_align/A1_translate_aln_codon_to_aa_macse.sh evolution_analysis/code/code_align/A0_translate_aln_codon_to_aa_macse.sh renamed to evolution_analysis/code/code_align/A1_translate_aln_codon_to_aa_macse.sh

@@ -10,7 +10,7 @@
 import os
 import argparse
 
-# other small task
+# others small task
 # compare the result after the tree pruner
 def removeStopCode(fasta_input, fasta_out):
     '''

evolution_analysis/code/code_align/A5_remove_stop_codon_commond_line.py

@@ -45,4 +45,4 @@ def main():
     main()
 
 # an example
-# python /Users/luho/Documents/evolution_analysis/code/code_align/A9_move_align_guidance_into_new_file.py -r /Users/luho/Documents/cds_align_guidance/ -n /Users/luho/Documents/cds_align_guidance_new/
+# python /Users/luho/Documents/evolution_analysis/code/code_align/A7_move_align_guidance_into_new_file.py -r /Users/luho/Documents/cds_align_guidance/ -n /Users/luho/Documents/cds_align_guidance_new/

…/A9_move_align_guidance_into_new_file.py …/A7_move_align_guidance_into_new_file.pyevolution_analysis/code/code_align/A9_move_align_guidance_into_new_file.py renamed to evolution_analysis/code/code_align/A7_move_align_guidance_into_new_file.py evolution_analysis/code/code_align/A9_move_align_guidance_into_new_file.py renamed to evolution_analysis/code/code_align/A7_move_align_guidance_into_new_file.py

@@ -155,4 +155,4 @@ def main():
     main()
 
 # usage
-# python A10_coden_align_filter_based_gap.py -n /Users/luho/Documents/branch_site_methanol/cds_align_macse_remove_stop_code_methanol/ -o /Users/luho/Documents/branch_site_methanol/cds_align_gap_filter_methanol/ -m /Users/luho/Documents/branch_site_methanol/coordinate_mapping_after_cds_filter/
+# python A8_coden_align_filter_based_gap.py -n /Users/luho/Documents/branch_site_methanol/cds_align_macse_remove_stop_code_methanol/ -o /Users/luho/Documents/branch_site_methanol/cds_align_gap_filter_methanol/ -m /Users/luho/Documents/branch_site_methanol/coordinate_mapping_after_cds_filter/

…lign/A10_coden_align_filter_based_gap.py …align/A8_coden_align_filter_based_gap.pyevolution_analysis/code/code_align/A10_coden_align_filter_based_gap.py renamed to evolution_analysis/code/code_align/A8_coden_align_filter_based_gap.py evolution_analysis/code/code_align/A10_coden_align_filter_based_gap.py renamed to evolution_analysis/code/code_align/A8_coden_align_filter_based_gap.py

@@ -13,7 +13,7 @@
 import os
 import argparse
 
-# other small task
+# others small task
 # compare the result after the tree pruner
 def removeStopCode(fasta_input, fasta_out):
     '''